I wanted to use NextMaSigPro package to study dynamics of gene expression over development. As part of this study is descriptive, I wanted to extract the information on how many genes increase expression over time, or decrease, or stay flat, etc.

To check this, I made a single series (only females) design matrix, with three replicates for each of the three-time points (quadratic regression). Then, I called p.vector() to get a regression fit for each gene. Out of 15 500 genes, 10 519, are significant. As my only variables, in this case, are Time and Time2, does this mean that 10 519 genes, change expression over time?

If that is the case, what exactly am I looking when I do stepwise regression, for variable selection? After stepwise regression, 4217 out of 10 519 genes are significant.